R Notebook

  objs.m <- MapObjects(objs.i[["Mouse"]], objs.i[["Opossum"]], c("subclass", "type"), assay = "integrated")

Warning: Both reference and query assays have been processed with SCTransform.Setting normalization.method = 'SCT' and continuing.Normalizing query using reference SCT model
Projecting cell embeddings
Finding neighborhoods
Finding anchors
    Found 224 anchors
Filtering anchors
    Retained 48 anchors
Finding integration vectors
Finding integration vector weights
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Predicting cell labels
Predicting cell labels
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')

  |                                                  | 0 % ~calculating  

Integrating dataset 2 with reference dataset
Warning: Number of anchors is less than k.weight. Lowering k.weight for sample pair.Finding integration vectors
Integrating data

  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Computing nearest neighbors
Running UMAP projection
10:14:19 Read 7123 rows
10:14:19 Processing block 1 of 1
10:14:19 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
10:14:20 Initializing by weighted average of neighbor coordinates using 1 thread
10:14:20 Commencing optimization for 167 epochs, with 213690 positive edges
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10:14:25 Finished
Warning: Both reference and query assays have been processed with SCTransform.Setting normalization.method = 'SCT' and continuing.Normalizing query using reference SCT model
Projecting cell embeddings
Finding neighborhoods
Finding anchors
    Found 298 anchors
Filtering anchors
    Retained 69 anchors
Finding integration vectors
Finding integration vector weights
Error in idx[i, ] <- res[[i]][[1]] : 
  number of items to replace is not a multiple of replacement length

obj.mouse <- ClusterSCT(obj.mouse, c(1))
obj.m.mouse <- ClusterSCT(obj.m.mouse, c(1))
obj.opossum <- ClusterSCT(obj.opossum, c(1))
obj.m.opossum <- ClusterSCT(obj.m.opossum, c(1))

obj.mouse <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_mouse.rds")

Loading required package: SeuratObject
Loading required package: sp

obj.opossum <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_opossum.rds")
objs.i.mouse <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_i_mouse.rds")
objs.i.opossum <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_i_opossum.rds")

DimPlot(obj.mouse, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.mouse, reduction = "umap", group.by = "subclass", label = TRUE, repel = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.mouse, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

obj.mouse$subclass.IT <- obj.mouse$subclass
obj.mouse$subclass.IT[obj.mouse$subclass %in% c("L2/3", "L4", "L5IT", "L6IT")] <-  "IT"
p <- DimPlot(obj.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.mouse, reduction = "umap", group.by = "subclass.IT", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_SubclassIT_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_SubclassIT_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.m.mouse, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

p <- DimPlot(obj.m.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.m.mouse, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_PredictedSubclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_PredictedSubclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.opossum, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.opossum, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

obj.opossum$subclass.IT <- obj.opossum$subclass
obj.opossum$subclass.IT[obj.opossum$subclass %in% c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E")] <-  "IT"
p <- DimPlot(obj.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.opossum, reduction = "umap", group.by = "subclass.IT", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_SubclassIT_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_SubclassIT_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.m.opossum, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
DimPlot(obj.m.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.opossum, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.opossum, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

PlotMapping(list(objs.m.mouse[[1]], objs.m.opossum[[1]]), ident.order = c("IT", "L2/3", "L4", "L5IT", "L6IT", "L5NP", "L5PT", "L6CT", "L6b"))

PlotMapping(list(objs.m.mouse[[2]], objs.m.opossum[[2]]), ident.order = c("Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Stac", "Meis2"))

PlotMapping(list(objs.m.mouse[[3]], objs.m.opossum[[3]]), ident.order = c("Astro", "Micro", "OD", "OPC", "Endo", "VLMC"))

Idents(objs.m.opossum[[1]]) <- "subclass"
levels(objs.m.opossum[[1]]) <- c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E", "L5NP", "L5PT", "L6CT", "L6b")
VlnPlot(objs.m.opossum[[1]], "predicted.subclass.score") + NoLegend()

Idents(objs.m.opossum[[2]]) <- "subclass"
levels(objs.m.opossum[[2]]) <- c("Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Meis2")
VlnPlot(objs.m.opossum[[2]], "predicted.subclass.score") + theme(legend.spacing.x = unit(2.0, 'cm'))

Idents(objs.m.opossum[[3]]) <- "subclass"
levels(objs.m.opossum[[3]]) <- c("Astro", "Micro", "OD", "OPC", "Endo", "VLMC")
VlnPlot(objs.m.opossum[[3]], "predicted.subclass.score") + theme(legend.spacing.x = unit(2.0, 'cm'))

Idents(obj.m.opossum) <- "subclass"
levels(obj.m.opossum) <- c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E", "L5NP", "L5PT", "L6CT", "L6b", 
                               "Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Meis2", 
                               "Astro", "Micro", "OD", "OPC", "Endo", "VLMC")
VlnPlot(obj.m.opossum, "predicted.subclass.score") + NoLegend()

saveRDS(obj.mouse, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_mouse.rds")
saveRDS(obj.opossum, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_opossum.rds")
saveRDS(objs.i.mouse, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_i_mouse.rds")
saveRDS(objs.i.opossum, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_i_opossum.rds")
saveRDS(objs.m.mouse, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/objs_m_mouse.rds")
saveRDS(objs.m.opossum, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/objs_m_opossum.rds")
saveRDS(obj.m.mouse, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_m_mouse.rds")
saveRDS(obj.m.opossum, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-Tasic/obj_m_opossum.rds")